Historical demographic change and interspecific gene flow are two of the most important factors that may highly affect genetic diversity. Thanks to simulation based on coalescent theory, we now can infer ancient population dynamics and gene flow via genetic data and understand how their contribution for current population/species. High endemism and potentially close phylogenetic relationship in Taiwanese skullcaps species (Genus Scutellaria) make them suitable for this study. Reconstruction of phylogenetic trees via both chloroplast and nuclear DNA sequences supports the idea of recent divergence of Taiwanese skullcaps, and suggested at least three-time origins of all Taiwanese skullcaps. Furthermore, four of seven Taiwanese species (S.indica, S.tashiroi, S. playfairii, and S. austrotaiwanensis) were chosen for this study because of their distributional and morphological similarities, and their closely phylogenetic relationship as well. These four species were suggested to be single originated and would be called "the indica group". DIVA analysis showed northern origin of indica group and indicated divergence with multiple dispersal and vicariance events mostly happening in interglacial periods. Species divergence during the warming interglacial periods was often thought to be the consequence of long-distance dispersal following population isolation. Both processes of dispersal and isolation resulted in such high speciation rate and high endemism of skullcaps in Taiwan. Indeed, long dispersal of skullcaps highly relied on environment force (ex: flood), and isolation or population divergence were often reported in skullcaps due to dynamic change of environments. In contrast to divergence, high degree of interspecific gene flow was detected under IM model using cpDNA and nuclear DNA sequences and microsatellite DNA, suggesting fluent gene flow in early divergence of Taiwanese skullcaps. However, low species admixture can be found in Bayesian clustering analysis by both microsatellites and AFLP. It might imply unhindered gene flow in the past but complete or well forming reproductive isolation between species nowadays. This may also explain the incongruence between chloroplast and nuclear markers and also understand these effects on genetic diversity among genetic regions.